[gmx-users] calculate potential with tabulated non-bonded interactions

Justin A. Lemkul jalemkul at vt.edu
Thu Nov 17 17:00:49 CET 2011

Liu, Liang wrote:
> Dear all,
> I am trying to calculate potentials for RNA structures with a serial of 
> tabulated potentials (non-bonded).
> And the only potential I am going to use is the tabulated potentials, 
> and the effect from force field should be removed.
> However, when I use pdb2gmx to build the topology file, I have to choose 
> a force field. What should I do for that? Thanks.

It sounds like you need to be constructing your own force field, completely, 
from scratch.  If you're not looking to use the existing force fields, this 
sounds like the only real solution.  You can take the time to make .xvg files 
for bonded and nonbonded interactions (see the manual), but that is probably 
just as much work and your simulations will be much slower.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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